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snpReportR: A Method for RNAseq Variant Detection Reporting
| Information | Value |
|---|---|
| Name: | Jane Doe |
| DOB: | 01/01/1900 |
| Sex: | F |
| Sample Type: | RNA |
| Information | Value |
|---|---|
| Name: | Dr.X |
| Doctor identification number: | 12345 |
| Hospital: | NCI |
This document will help you to understand the more important findings from a gene variant screening. The common definitions of the type of genetic variants (mutations) are described in the figure and in the table in section Chromosome and Gene Vizualization of Mutations.
While a variant may have been detected, the associations with the variant are not perfectly causal and their complex interactions between biology and the environment.
Table 1. Column names and Descriptions
In addition there are functional annotations for the variants per transcript from snpEFF. These include:
The top variants were ranked by the following attributes:
Interpretation of attributes
## [1] "KRAS" "KEAP1" "PLK1" "FUS" "PDIA6"
Expression of Genes with identified variants/SNVs in Normal Tissues.
Included here are two tables for different gene types. Coding refers to genes that produce proteins, while non-coding refers to genes which do get utilized to produce proteins.
| Type | Description |
|---|---|
| coding: | Mutation is within a coding region |
| 5prime_UTR: | Mutation is within 5’ untranslated region |
| 3prime_UTR: | Mutation is with 3’ untranslated region |
| introninc: | Mutation is with an intron region |
| splice: | Mutation is within proximity to a splice-site. |
| synonymous_variant: | Synonymous variant is a mutation in an exon that results in same amino acid (changed codon) |
| missense_variant: | Missense variant is a mutation in an exon that results in a different amino acid (changed codon) |
| start/stop: | Mutation is within a start/stop codon. |
Figure 1. Percentage of different types of mutations identified.
# Add Lollipop plot - interactive| Symbol | GeneID | DRR132310_H1299_1.0.bam | DRR132321_H1299_0.1.bam | DRR132333_H1299_.01.bam | DRR131576_A549_1.0.bam | DRR131588_A549_0.1.bam | DRR131599_A549_.01.bam |
|---|---|---|---|---|---|---|---|
| TACC2 | 10579 | 3.49 | 4.54 | 4.63 | 5.25 | 3.67 | 4.94 |
| KRAS | 3845 | 5.73 | 6.20 | 5.57 | 5.94 | 4.44 | 5.73 |
| PLK1 | 5347 | 8.96 | 8.87 | 9.14 | 8.85 | 8.64 | 8.91 |
| FUS | 2521 | 8.08 | 8.07 | 7.73 | 7.42 | 7.68 | 7.16 |
| SLC25A11 | 8402 | 6.14 | 6.52 | 6.28 | 7.93 | 8.11 | 8.01 |
| KEAP1 | 9817 | 7.07 | 7.40 | 6.81 | 6.85 | 6.62 | 7.54 |
| GPATCH1 | 55094 | 5.37 | 5.33 | 5.28 | 5.45 | 0.62 | 4.67 |
| PDIA6 | 10130 | 8.11 | 7.93 | 8.24 | 9.17 | 8.74 | 9.00 |
| TCEA2 | 6919 | 2.76 | 1.21 | 3.22 | 3.67 | 0.62 | 2.76 |
| CD2AP | 23607 | 6.53 | 6.23 | 6.01 | 5.62 | 4.67 | 5.20 |
| FUCA2 | 2519 | 8.50 | 8.50 | 8.34 | 7.64 | 8.37 | 8.12 |
| FGL1 | 2267 | 0.62 | 0.62 | 0.62 | 7.15 | 7.12 | 6.66 |
Expression of the genes with pathogenic variants identified.
# add results hereGenetic tests sometimes reveal information that could be relevant to your family such as a health risk that might run in the family, or that family relationships are different from what you expected.
Can you please add this message in the next steps section, if the report show an association with a gene. Please contact your doctor and a genetic counselor. A genetic counselor can help you understand:
# Need diagram hereCan search for additional drugs that may target the mutant genes online using Drug Targetor and at Drug Gene Interaction Database
# add drug target data information# search API at https://clinicaltrials.gov/api/# Add QR code where does it go?This should simply be a copy of the consent form the patient has already signed. Also, interactive shiny widgets make this less portable.
# embed file here# include Deeptools plots for coverage, average
# base quality scores, alignment quality scores,
# etc.Smith RN, et al. InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data. Bioinformatics. 2012 Dec 1;28(23):3163-5.
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